KDM2B

Chr 12q24.31

lysine demethylase 2B

Aliases:: PCCX2, CXXC2, Fbl10, JHDM1B
MANE:: ENST00000377071.9

OMIM: 609078 ↗NCBI: 84678 ↗Ensembl ↗

Annotations refreshed 9 hours ago.

Predicted protein structure

AlphaFold predicted structure

KDM2B · Q8NHM5

v62025-08-01

Predicted Aligned Error matrix for KDM2B — diagonal shows residue index, colour shows pairwise prediction confidence (lower is better) — Predicted Aligned Error

Mean pLDDT

67.8/ 100

Low

1,336 residues

Confidence breakdown

Very high(≥ 90)38%
Confident(70–90)19%
Low(50–70)4%
Very low(< 50)39%

Open interactive 3D viewer

AlphaFold (Jumper et al., 2021) · CC BY 4.0

Clinical relevance (Genomics England PanelApp)

Diagnostic Grade (Green)

DDG2P
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Fetal anomalies
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Intellectual disability
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Disease associations (Open Targets)

hypertensive disorder
0.44
hereditary disease
0.42
essential hypertension
0.39
type 2 diabetes mellitus
0.38
diabetes mellitus
0.37
neurodegenerative disease
0.36
diabetic eye disease
0.30
diabetic retinopathy
0.30
Increased blood pressure
0.29
Global developmental delay
0.26

Score is the Open Targets composite evidence score (0-1). Higher = stronger gene-disease association.

Protein function (UniProt)

Lysine-specific demethylase 2B

Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36' (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation (PubMed:16362057, PubMed:17994099). May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin ligase complex (Probable)